Just came across this issue on our cluster which is using an intel compiled version of R. Since the problem is timezone related, perhaps a suitable patch would be to just return UTC times when the intel compiler is in use. These won't be incorrect, just a little less friendly.

Sorry for the delay. I just made a change to S4Vectors that might address this. The change is in versions 0.6.4 (release) and 0.7.14 (devel) which should become available via biocLite() in the next 24 hours or less. I don't have access to the Intel Compiler though so I was not able to test this. Would be great if you could give it a try and let me know. Thanks in advance!